The following pages and posts are tagged with
| Title | Type | Excerpt |
|---|---|---|
| Acknowledgements | Page | Anchor’s author is Owen Feehan. Particular additional thanks to: ETH Zurich, the late Prof. Wilhelm Krek in whose lab the software originated for analyzing microscopy images. Many members of the Institute of Molecular Health Sciences who kindly helped in associated research and became the first... |
| Developer Guide - Getting started | Page | Code architecture and API Architecture Overview - how the different repositories and JARs relate to each other. Javadoc Key systems GitHub - hosts all source code, the website, JAR artifacts, continuous integration, and issues and projects. SonarCloud - static code... |
| Developer Guide - Anchor distribution | Page | What is an Anchor distribution? An Anchor distribution is a folder which contains all the jars and configuration-files to run Anchor. It has the following structure: Folder Description bin/ anchor-launcher.jar and associated helper-applications lib/ other anchor... |
| Developer Guide - Building Anchor | Page | Maven Anchor uses Apache Maven as a build tool. As a prior step, Maven should be installed locally, configured for the Anchor project. Assembly The anchor-assembly is a special module that doesn’t generate a .jar artifact, but rather assembles the output of other modules (artifacts) into... |
| Download | Page | Anchor can be downloaded as a distribution (zip or tar.gz). This must be unpacked into a directory, followed by setting some environment variables. Please download the latest version (anchor-0.12-prerelease) from GitHub, as matches your operating system: Windows MacOS Linux <i... |
| Installation | Page | Anchor is a command-line application, designed to be used with PowerShell / Command Prompt in Windows, Terminal in MacOS or any Linux shell. Quick Instructions Download, unzip, and add the bin/ directory to $PATH environmental variable.... |
| Installation - Detailed Instructions | Page | Anchor is a command-line application, designed to be used with PowerShell / Command Prompt in Windows, Terminal in MacOS or any Linux shell. It should be added to the system’s PATH environmental variable. Steps 1. Download and unpack... |
| User Guide - Essentials | Page | ## Essentials of Anchor ### Experiments are inputs, task, outputs An experiment is *roughly-speaking* the execution of a [task](/user_guide_tasks.html) on **inputs** to produce **outputs**. ``` outputs = task(inputs) ``` Inputs are usually images (or images plus extras). Outputs can be images, text-files, CSVs, XML or any other file-type. {% include... |
| User Guide - BeanXML | Page | ## What is BeanXML? BeanXML is a type of XML used by Anchor to define experiments, configuration and many aspects of behaviour. It is flexible and extensible, and can easily be used with new types of plugins and other objects, as they are developed and added to Anchor. {% include... |
| User Guide - Command line | Page | ## Introduction Anchor can be used from the command-line as follows: ```shell anchor [options] [experimentFile.xml] ``` If an `experimentFile.xml` isn't specified, the [default experiment](/user_guide.html#defaultExperiment) is employed, with default *inputs*, [task](/user_guide_tasks.html), *outputs*. ## Major options The **most important** command-line options are: | Option | Description| |----------|------------| | -i *arg* | [Changes... |
| User Guide - Supported image formats | Page | ## Supported image types ### Images are diverse We intuitively think of an image file as a digital photograph, similar in appearance to human vision, containing a matrix of RGB or grayscale pixels. In reality, images come in diverse form: varying in dimension, number of channels, color depth and type,... |
| User Guide - Tasks | Page | ## Tasks A task is a unit of processing, applied to one or more inputs, and producing derived outputs. {% include tip.html content="Each task accomplishes one goal - either its is entirety, or as single step towards a greater goal, like a single step in a pipeline of image processing... |
| User Guide - Troubleshooting | Page | ## Troubleshooting Image processing is often resource-heavy and computational demanding. Anchor runs jobs in parallel, and issues often arise. Here are some tips to resolve common issues. ### Limiting parallel CPU cores By default, Anchor uses all-except-once available CPU cores to execute operations in parallel. Some [tasks](/user_guide_tasks.html) require more memory... |